If you can get the clones into another folder, you could use mass renaming to add something like .hide to the end of the file names. You could then reintegrate the files and Emulation Station would ignore them. Keep in mind that some clones are highly desireable, like pacman.zip for example, or all the two player alternates to four player games that won't allow character selection outside of remapping.

For the reason you mentioned, sometimes I would like to see the clones. So what I am seeking is an option "Hide clones - on/off" that I can toggle, so that I can show or hide clones within ES.

I think the gamelist.xml scraper files should already contain the information about which games are clones.

In general I am missing more display options, like what I have in Mamextras on my Xbox already: I want to filter only 2 player games, or only 4 player games, only clones, only parents, only fighting games, only games starting with a, etc...

What is the point of all the scraping if the game lists can't be filtered?

So what I am seeking is an option "Hide clones - on/off" that I can toggle, so that I can show or hide clones within ES.

In general I am missing more display options, like what I have in Mamextras on my Xbox already: I want to filter only 2 player games, or only 4 player games, only clones, only parents, only fighting games, only games starting with a, etc...

Nothing like that currently exists in Emulation Station.

What is the point of all the scraping if the game lists can't be filtered?

To look pretty. ;)

Emulation Station serves as an arcade launching alternative and is designed to cover a lot of ground for many emulators. It was never intended to be a feature-by-feature replacement for other emulator-specific launchers. If those sorting features are important to you, then I would look elsewhere. Alternatively, if you have the ability, you could add them yourself and submit a PR to be considered for inclusion in RetroPie.

In general I am missing more display options, like what I have in Mamextras on my Xbox already: I want to filter only 2 player games, or only 4 player games, only clones, only parents, only fighting games, only games starting with a, etc...

EmulationStation does support filtering by the metadata so you can filter by player count or genre. However, clone/parent status is not part of the metadata that ES is aware of so you cannot filter on those. The filter options are available in the menu when you press 'select'.